Add ability to add/edit/remove line items, including adjustment of prices, qty, variant. Less important, but nice would be ability to override override adjustments and/or order total.
This would especially make sense if you use manual payments. A customer of mine does not know shipping rates in advance, so she only accepts manual payments... this was in expresso store... now I would like to migrate the store to commerce, but this feature would have to be available for this particular store. Believe it or not but in some countries only few people have credit cards... o-O